Molecular inversion probes (MIPs) can be used to capture targeted regions of a person's genetic material and to assay for disease-associated mutations. Each MIP has two linked oligonucleotide targeting arms that are designed to hybridize to a strand of nucleic acid in positions that flank a region of interest. In a typical assay, a set of MIPs is used to cover a gene segment of interest. Most of the MIPs hybridize to their intended target. Upon successful hybridization, the two targeting arms of one MIP are connected together in a ligation step into a covalently closed circle. Such assays are useful in interrogating the genome for mutations such as single-nucleotide polymorphisms.
Unfortunately, some mutations such as unexpected deletions, insertions, translocations, or inversions may be associated with an absent or incomplete targeting arm hybridization site and thus interfere with the ability of the MIPs to hybridize and be circularized. Unbound DNA and un-circularized MIPs are typically digested away by an exonuclease after which the circularized MIPs are used in amplification or sequencing reactions.